Published in J R Soc Interface on March 14, 2012
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Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission. Mol Biol Evol (2013) 1.88
Estimating the basic reproductive number from viral sequence data. Mol Biol Evol (2011) 1.86
Stable virulence levels in the HIV epidemic of Switzerland over two decades. AIDS (2006) 1.81
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Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLoS Pathog (2010) 1.63
Stochastic or deterministic: what is the effective population size of HIV-1? Trends Microbiol (2006) 1.58
An evolutionary scenario for the transition to undifferentiated multicellularity. Proc Natl Acad Sci U S A (2003) 1.55
The evolution of connectivity in metabolic networks. PLoS Biol (2005) 1.54
Recombination in HIV and the evolution of drug resistance: for better or for worse? Bioessays (2004) 1.54
Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland. Clin Infect Dis (2009) 1.50
Inferring epidemic contact structure from phylogenetic trees. PLoS Comput Biol (2012) 1.47
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Estimating the stoichiometry of human immunodeficiency virus entry. J Virol (2008) 1.36
Quantification of infectious HIV-1 plasma viral load using a boosted in vitro infection protocol. Virology (2004) 1.32
Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods. Philos Trans R Soc Lond B Biol Sci (2013) 1.31
Simulating the evolution of signal transduction pathways. J Theor Biol (2006) 1.31
The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off. Microbiology (2005) 1.30
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The state of affairs in the kingdom of the Red Queen. Trends Ecol Evol (2008) 1.23
Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1. J Virol (2005) 1.18
Human immunodeficiency virus type 1 fitness is a determining factor in viral rebound and set point in chronic infection. J Virol (2003) 1.18
Rapid parasite adaptation drives selection for high recombination rates. Evolution (2007) 1.18
Exploring the complexity of the HIV-1 fitness landscape. PLoS Genet (2012) 1.17
Evolution of complexity in signaling pathways. Proc Natl Acad Sci U S A (2006) 1.14
Effect of varying epistasis on the evolution of recombination. Genetics (2006) 1.14
Humoral immunity to HIV-1: kinetics of antibody responses in chronic infection reflects capacity of immune system to improve viral set point. Blood (2004) 1.14
The effect of population structure on the emergence of drug resistance during influenza pandemics. J R Soc Interface (2007) 1.12
Rapid viral decay in simian immunodeficiency virus-infected macaques receiving quadruple antiretroviral therapy. J Virol (2006) 1.10
African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study. AIDS (2009) 1.08
Assessing predicted HIV-1 replicative capacity in a clinical setting. PLoS Pathog (2011) 1.06
The effect of multifunctionality on the rate of evolution in yeast. Mol Biol Evol (2005) 1.06
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The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland. J Infect Dis (2011) 1.03
Red Queen dynamics with non-standard fitness interactions. PLoS Comput Biol (2009) 1.03
Compensation of fitness costs and reversibility of antibiotic resistance mutations. Antimicrob Agents Chemother (2010) 1.01
Residual viral replication during antiretroviral therapy boosts human immunodeficiency virus type 1-specific CD8+ T-cell responses in subjects treated early after infection. J Virol (2002) 0.97
Virus evolution: the importance of being erroneous. Nature (2002) 0.97
The evolution of network topology by selective removal. J R Soc Interface (2005) 0.96
Evolution of stress response in the face of unreliable environmental signals. PLoS Comput Biol (2012) 0.96
Mutation accumulation in space and the maintenance of sexual reproduction. Ecol Lett (2006) 0.96
Signal transduction networks: topology, response and biochemical processes. J Theor Biol (2005) 0.95
The role of epistasis on the evolution of recombination in host-parasite coevolution. Theor Popul Biol (2008) 0.94
High epitope expression levels increase competition between T cells. PLoS Comput Biol (2006) 0.93
On being the right size: the impact of population size and stochastic effects on the evolution of drug resistance in hospitals and the community. PLoS Pathog (2011) 0.93
Spatial models of virus-immune dynamics. J Theor Biol (2004) 0.93
Informed switching strongly decreases the prevalence of antibiotic resistance in hospital wards. PLoS Comput Biol (2011) 0.93
Bottleneck-induced transitions in a minimal model for intracellular transport. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.92
The role of recombination for the coevolutionary dynamics of HIV and the immune response. PLoS One (2011) 0.92
Viral dynamics and in vivo fitness of HIV-1 in the presence and absence of enfuvirtide. J Acquir Immune Defic Syndr (2008) 0.92
Decelerating decay of latently infected cells during prolonged therapy for human immunodeficiency virus type 1 infection. J Virol (2002) 0.92
The Red Queen and the persistence of linkage-disequilibrium oscillations in finite and infinite populations. BMC Evol Biol (2007) 0.91
On the causes of selection for recombination underlying the red queen hypothesis. Am Nat (2009) 0.90
Modelling cytomegalovirus replication patterns in the human host: factors important for pathogenesis. Proc Biol Sci (2006) 0.90
Recombination and drug resistance in HIV: population dynamics and stochasticity. Epidemics (2008) 0.90
Guanine-adenine bias: a general property of retroid viruses that is unrelated to host-induced hypermutation. Trends Genet (2005) 0.88
Bacterial growth properties at low optical densities. Antonie Van Leeuwenhoek (2009) 0.87
Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics. Epidemics (2012) 0.84
Contribution of peaks of virus load to simian immunodeficiency virus pathogenesis. J Virol (2002) 0.84
Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland. Am J Epidemiol (2014) 0.83
Contribution of recombination to the evolutionary history of HIV. Curr Opin HIV AIDS (2015) 0.82
HIV coreceptor usage and drug treatment. J Theor Biol (2002) 0.82
HIV replication elicits little cytopathic effects in vivo: analysis of surrogate markers for virus production, cytotoxic T cell response and infected cell death. J Med Virol (2006) 0.82
Nested model reveals potential amplification of an HIV epidemic due to drug resistance. Epidemics (2012) 0.82
Plasmids and evolutionary rescue by drug resistance. Evolution (2014) 0.81
Weighting for sex acts to understand the spread of STI on networks. J Theor Biol (2012) 0.81
Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution. Epidemics (2013) 0.81
Principal component analysis of general patterns of HIV-1 replicative fitness in different drug environments. Epidemics (2010) 0.81
Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase. PLoS Comput Biol (2012) 0.81
Short communication: HIV type 2 dynamics. AIDS Res Hum Retroviruses (2005) 0.80
Epitope down-modulation as a mechanism for the coexistence of competing T-cells. J Theor Biol (2004) 0.80
Fixation probability of mobile genetic elements such as plasmids. Theor Popul Biol (2013) 0.79
Predicting the evolution of sex on complex fitness landscapes. PLoS Comput Biol (2009) 0.78
The impact of vaccination on the breadth and magnitude of the antibody response to influenza A viruses in HIV-infected individuals. AIDS (2015) 0.78
Can high-risk fungicides be used in mixtures without selecting for fungicide resistance? Phytopathology (2014) 0.78
On the evolution of sexual reproduction in hosts coevolving with multiple parasites. Evolution (2010) 0.77
A Method to Estimate the Size and Characteristics of HIV-positive Populations Using an Individual-based Stochastic Simulation Model. Epidemiology (2016) 0.75
On the role of resonance in drug failure under HIV treatment interruption. Theor Biol Med Model (2013) 0.75
Evaluation of the Predictive Potential of the Short Acute Retroviral Syndrome Severity Score for HIV-1 Disease Progression in Individuals With Acute HIV Infection. J Acquir Immune Defic Syndr (2017) 0.75
Response to Bandeira and Faro: Closing the circle of constraints. Trends Immunol (2003) 0.75
Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T Cell Decline and Per-Parasite Pathogenicity. Mol Biol Evol (2017) 0.75
Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe. PLoS Biol (2017) 0.75
Prescription of Post-Exposure Prophylaxis for HIV-1 in the emergency room: Correct transmission risk assessment remains challenging. J Acquir Immune Defic Syndr (2016) 0.75